Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers

BACKGROUND

The frequency with which targeted tumor sequencing results will lead to implemented change in care is unclear. Prospective assessment of the feasibility and limitations of using genomic sequencing is critically important.

METHODS

A prospective clinical study was conducted on 100 patients with diverse-histology, rare, or poor-prognosis cancers to evaluate the clinical actionability of a Clinical Laboratory Improvement Amendments (CLIA)-certified, comprehensive genomic profiling assay (FoundationOne), using formalin-fixed, paraffin-embedded tumors. The primary objectives were to assess utility, feasibility, and limitations of genomic sequencing for genomically guided therapy or other clinical purpose in the setting of a multidisciplinary molecular tumor board.

RESULTS

Of the tumors from the 92 patients with sufficient tissue, 88 (96%) had at least one genomic alteration (average 3.6, range 0-10). Commonly altered pathways included p53 (46%), RAS/RAF/MAPK (rat sarcoma; rapidly accelerated fibrosarcoma; mitogen-activated protein kinase) (45%), receptor tyrosine kinases/ligand (44%), PI3K/AKT/mTOR (phosphatidylinositol-4,5-bisphosphate 3-kinase; protein kinase B; mammalian target of rapamycin) (35%), transcription factors/regulators (31%), and cell cycle regulators (30%). Many low frequency but potentially actionable alterations were identified in diverse histologies. Use of comprehensive profiling led to implementable clinical action in 35% of tumors with genomic alterations, including genomically guided therapy, diagnostic modification, and trigger for germline genetic testing.

CONCLUSION

Use of targeted next-generation sequencing in the setting of an institutional molecular tumor board led to implementable clinical action in more than one third of patients with rare and poor-prognosis cancers. Major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access. Early and serial sequencing in the clinical course and expanded access to genomically guided early-phase clinical trials and targeted agents may increase actionability.

IMPLICATIONS FOR PRACTICE

Identification of key factors that facilitate use of genomic tumor testing results and implementation of genomically guided therapy may lead to enhanced benefit for patients with rare or difficult to treat cancers. Clinical use of a targeted next-generation sequencing assay in the setting of an institutional molecular tumor board led to implementable clinical action in over one third of patients with rare and poor prognosis cancers. The major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access both on trial and off label. Approaches to increase actionability include early and serial sequencing in the clinical course and expanded access to genomically guided early phase clinical trials and targeted agents.

Comprehensive genomic profiling of anal squamous cell carcinoma reveals distinct genomically defined classes

BACKGROUND

Squamous cell cancers of the anal canal (ASCC) are increasing in frequency and lack effective therapies for advanced disease. Although an association with human papillomavirus (HPV) has been established, little is known about the molecular characterization of ASCC. A comprehensive genomic analysis of ASCC was undertaken to identify novel genomic alterations (GAs) that will inform therapeutic choices for patients with advanced disease.

PATIENTS AND METHODS

Hybrid-capture-based next-generation sequencing of exons from 236 cancer-related genes and intronic regions from 19 genes commonly rearranged in cancer was performed on 70 patients with ASCC. HPV status was assessed by aligning tumor sequencing reads to HPV viral genomes. GAs were identified using an established algorithm and correlated with HPV status.

RESULTS

Sixty-one samples (87%) were HPV-positive. A mean of 3.5 GAs per sample was identified. Recurrent alterations in phosphoinositol-3-kinase pathway (PI3K/AKT/mTOR) genes including amplifications and homozygous deletions were present in 63% of cases. Clinically relevant GAs in genes involved in DNA repair, chromatin remodeling, or receptor tyrosine kinase signaling were observed in 30% of cases. Loss-of-function mutations in TP53 and CDKN2A were significantly enhanced in HPV-negative cases (P < 0.0001).

CONCLUSIONS

This is the first comprehensive genomic analysis of ASCC, and the results suggest new therapeutic approaches. Differing genomic profiles between HPV-associated and HPV-negative ASCC warrants further investigation and may require novel therapeutic and preventive strategies.

Comprehensive Genomic Profiling of Advanced Penile Carcinoma Suggests a High Frequency of Clinically Relevant Genomic Alterations

BACKGROUND

Advanced penile squamous cell carcinoma (PSCC) is associated with poor survival due to the aggressiveness of the disease and lack of effective systemic therapies. Comprehensive genomic profiling (CGP) was performed to identify clinically relevant genomic alterations (CRGAs).

MATERIALS AND METHODS

DNA was extracted from 40 μm of formalin-fixed, paraffin-embedded sections in patients with advanced PSCC. CGP was performed on hybridization-captured, adaptor ligation-based libraries to a mean coverage depth of 692× for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer. CRGAs were defined as genomic alterations (GAs) linked to targeted therapies on the market or under evaluation in mechanism-driven clinical trials.

RESULTS

Twenty male patients with a median age of 60 years (range, 46-87 years) were assessed. Seventeen (85%) cases were stage IV and three cases (15%) were stage III. CGP revealed 109 GAs (5.45 per tumor), 44 of which were CRGAs (2.2 per tumor). At least one CRGA was detected in 19 (95%) cases, and the most common CRGAs were CDKN2A point mutations and homozygous deletion (40%), NOTCH1 point mutations and rearrangements (25%), PIK3CA point mutations and amplification (25%), EGFR amplification (20%), CCND1 amplification (20%), BRCA2 insertions/deletions (10%), RICTOR amplifications (10%), and FBXW7 point mutations (10%).

CONCLUSION

CGP identified CRGAs in patients with advanced PSCC, including EGFR amplification and PIK3CA alterations, which can lead to the rational administration of targeted therapy and subsequent benefit for these patients.

IMPLICATIONS FOR PRACTICE

Few treatment options exist for patients with advanced penile squamous cell carcinoma (PSCC). Outcomes are dismal with platinum-based chemotherapy, with median survival estimated at 1 year or less across multiple series. Biological studies of patients with PSCC to date have principally focused on human papillomavirus status, but few studies have elucidated molecular drivers of the disease. To this end, comprehensive genomic profiling was performed in a cohort of 20 patients with advanced PSCC. Findings of frequent mutations in CDKN2A, NOTCH1, PIK3CA, and EGFR (all in excess of 20%) point to potential therapeutic avenues. Trials of targeted therapies directed toward these mutations should be explored.

Activating PIK3CA Mutations Induce an Epidermal Growth Factor Receptor (EGFR)/Extracellular Signal-regulated Kinase (ERK) Paracrine Signaling Axis in Basal-like Breast Cancer

Mutations in PIK3CA, the gene encoding the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K) have been shown to transform human mammary epithelial cells (MECs). These mutations are present in all breast cancer subtypes, including basal-like breast cancer (BLBC). Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 72 protein expression changes in human basal-like MECs with knock-in E545K or H1047R PIK3CA mutations versus isogenic MECs with wild-type PIK3CA. Several of these were secreted proteins, cell surface receptors or ECM interacting molecules and were required for growth of PIK3CA mutant cells as well as adjacent cells with wild-type PIK3CA. The proteins identified by MS were enriched among human BLBC cell lines and pointed to a PI3K-dependent amphiregulin/EGFR/ERK signaling axis that is activated in BLBC. Proteins induced by PIK3CA mutations correlated with EGFR signaling and reduced relapse-free survival in BLBC. Treatment with EGFR inhibitors reduced growth of PIK3CA mutant BLBC cell lines and murine mammary tumors driven by a PIK3CA mutant transgene, all together suggesting that PIK3CA mutations promote tumor growth in part by inducing protein changes that activate EGFR.

Abstract PD6-5: Profiling of ESR1-mutated metastatic breast cancers by FoundationOne® allows a broad genomic understanding for potential clinical implications

Background: Estrogen receptor (ER) inhibition is an important treatment option for advanced breast cancer (BC) pts. Recent studies describe recurring somatic mutations in codons 537 and 538 within the ligand-binding domain (LBD) of ∼ 20% of ER+ metastatic disease, but not treatment-naïve ER+ cancer or ER-negative disease, that render the ER constitutively active and confer partial resistance to endocrine agents. Few studies have described the clinicopathologic and genomic covariates that accompany the ESR1 genomic alterations (GAs). Correlating genomic events as captured by FoundationOne in pts with ESR1-mutated BCs with clinical history may provide clinical insight into these alterations.

Methods: Hybridization capture of 3769 exons of 236 cancer-related genes and 47 introns from 19 genes that are frequently rearranged in cancer were fully sequenced to high, uniform coverage using FoundationOne (Foundation Medicine, Cambridge, MA).

Results: 176 of the 2,208 (7.9%) BC pt cases harbored ESR1 alterations. 1127 short variants (SV) were detected in 176 patient samples for an average of 6.4 GA/sample. 16.5% SV (186/1127) were ESR1 GAs with an average of 1.0 ESR1 GAs/sample. ESR1 GAs consisted of base substitutions (77%) and amplifications (20%, median copy number 9X, range 6-28). Base substitutions occurred at codons 538 (71/145) and 537 (70/145) and at two other novel sites, 341 (2/145) and 563 (1/145). A patient-derived xenograft study suggested that tumors refractory to ER inhibitors and harboring ESR1 amplification could be responsive to higher doses of estradiol. (Li et al, Cell Reports, 2013). The most frequently co-occurring GAs were PIK3CA (37.5%), GATA3 (22.7%), TP53 (24.4%), MAP3K1 (10.2%) and CDH1 (7.9). Collection of data on tissue sites sequenced, treatments and outcomes on these pts with ESR1 GAs are ongoing. Of note, one pt had recurrent disease following adjuvant tamoxifen and letrozole. FoundationOne testing of her recurrent bony disease revealed an ESR1 Y537 alteration along with mutations in PIK3CA, APC, and RAD51. She has been on fulvestrant monotherapy with stable metastatic disease 13 + months.

Conclusions: We found through FoundationOne testing that ESR1 GAs are reasonably common in advanced BCs, with base substitutions accounting for 77% of ESR1 GAs and amplifications for 20%. Identification and characterization of ESR1-mutated advanced BC pts by comprehensive genomic profiling capable of detecting both base substitutions and copy number changes may identify clinically relevant GAs. Clinical correlation is pending.

Citation Format: Norma A Palma, Siraj Ali, Garrett Frampton, Kai Wang, Hannah Gilmore, Julio Peguero, Lyndsay N Harris, Massimo Cristofanilli, Juliann Chmielecki, Jeffrey S Ross, Deborah Morosini, Vincent A Miller, Phil J Stephens, Gary Palmer, Joyce O'Shaughnessy. Profiling of ESR1-mutated metastatic breast cancers by FoundationOne® allows a broad genomic understanding for potential clinical implications [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD6-5.

Abstract P2-03-06: FoundationOne profiling of TSC1 and TSC2-mutated advanced breast cancers

Background: The TSC1/TSC2 complex inhibits the mTOR pathway. Loss of function of this complex leads to hyperperactivation of the mTOR pathway which promotes growth and survival. Few studies have examined the role of TSC1 and TSC2 mutations in breast cancer and as a clinically relevant target for molecularly targeted therapy, such as everolimus, a rapamycin analog.

Methods: Hybridization capture of 3769 exons of 236 cancer-related genes and 47 introns from 19 genes that are frequently rearranged in cancer were fully sequenced to high, uniform coverage from a commercial CLIA-certified laboratory (Foundation Medicine).

Results: 30 of 2,208 breast cancer pt samples (1.3%) harbored either TSC1 (13/30, 43%) or TSC2 (17/30, 56%) genomic alterations (GAs). The samples with TSC1/2 consisted of breast carcinoma n.o.s. (17/30) and invasive ductal carcinoma (12/30); one invasive lobular carcinoma (ILC) harbored a TSC2 alteration. Sequencing was performed on metastatic (18/30, 60%) and primary (12/30, 40%) tumors. All TSC1 alterations resulted in truncation of the protein product; TSC2 GA consisted of truncations (14/17) and point mutations (3/17). TSC1/2 GAs frequently co-occurred with GAs in TP53 (19/30; 63%) and amplifications of MYC (9/30; 30%) and FGFR1 (7/30; 23%). Of the TSC1/2-mutant cases where hormone receptor and HER2/neu status was known (23/30), 65% were ER-/PR-/HER2- (TNBC), 26% were ER+/HER2- and 9% were ER-/HER2+.

Patient case: We describe a postmenopausal node positive ILC (ER+/PR+/HER2-) pt who received adjuvant chemotherapy followed by 9 yrs adjuvant anastrazole then with disease recurrence. On FoundationOne testing a TSC2 A1141T missense mutation, along with GAs in CDH1, ETV6, and CSF1R, were found in her metastatic disease in the soft tissues of her left orbit associated with substantial swelling resulting in loss of vision. While TSC2 A1141T has not been functionally characterized, in vitro and in vivo data suggest sensitivity to mTOR inhibitors. Her disease stabilized but did not decrease in size with vinorelbine + capecitabine. She was treated with letrozole + everolimus and had a near clinical complete response with restoration of vision for 5 + months. Collection of clinical data on additional pts is currently ongoing.

Conclusion: 1.3% of breast cancer cases harbored GAs in either TSC1 orTSC2. The majority of TSC1/2 GAs cause inactivation of these negative regulatory proteins leading to activation of the mTOR signaling pathway. TSC1/2 GAs were enriched for TNBC (65%) versus non-TNBC (35%) (p= 0.077; Fisher’s exact test). Truncation of TSC1/2 occurred at multiple codons, underscoring the importance of examining the entire coding region of tumor suppressor genes for these inactivating events. Comprehensive genomic profiling has the potential to identify the broad spectrum of these inactivating events, a subset of which may be clinically relevant.

Citation Format: Norma A Palma, Juliann Chmielecki, Garrett Frampton, Siraj Ali, Maren Levin, Jeffrey S Ross, Deborah Morosini, Gary Palmer, Vincent A Miller, Phil Stephens, Joyce O'Shaughnessy. FoundationOne profiling of TSC1 and TSC2-mutated advanced breast cancers [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-06.

Abstract P6-14-02: Genomic profiling by FoundationOne® analysis of inflammatory breast cancer cases reveals a high frequency of clinically relevant genomic alterations (GA)

Background: Inflammatory breast cancer (IBC) is a distinct clinicopathologic entity that carries a worse prognosis relative to non-IBC breast cancer even when matched for biomarkers (ER/PR/HER2). Genomic profiling of IBC cases may identify alterations that suggest response to targeted therapies, but is best implemented by an integrated NGS assay capable of detecting all classes of genomic alterations (GA).

Methods: Hybridization capture of 3769 exons of 236 cancer-related genes and 47 introns from 19 genes that are frequently rearranged in cancer were fully sequenced to high, uniform coverage from a commercial CLIA-certified laboratory (Foundation Medicine).

Results: Of 2,208 clinical breast cancer cases assayed, 55 IBC cases were identified, and of the 50 cases for which hormone receptor and HER2/neu status were know, 34% were ER-/PR-/HER2- (TNBC). IBC cases harbored 274 GA with an average of 5.0 GA/tumor (range 1-15). At least one alteration associated with an FDA approved therapy or clinical trial was identified in 53/55 (96%) of cases, yielding an average of 2.6 clinically relevant GA/case. Genes most frequently altered were TP53 (60%), MYC (31%), PIK3CA (25%), ERBB2 (20%), FGFR1 (18%) and PTEN (16%). MYC amplifications were present in 24% of the 2,208 clinical breast carcinoma cases. In the TNBC subset of IBC, 8/19 (42%) pt samples showed MYC amplification (median copy number 8X, range 7-20) as compared to 9/36 (25%) in non-TNBC pt samples (median copy number 7X, range 6-21).

Within this prospective series, treatment decisions were made based on FoundationOne results. A58-year old pt with likely secondary IBC harbored two ERBB2 activating base substitutions (V777L and S310F), but without amplification of ERBB2), and had durable response to lapatinib (Ali et al. JCO 2014). In another case, a 53 year old pt presented with ERBB2-amplified IBC now refractory to HER2-targeted therapy. FoundationOne testing revealed an activating EGFR mutation (L858R) as well as the previously described ERBB2 amplification, suggesting that the EGFR alteration may underlie the acquired resistance. The pt responded to erlotinib monotherapy for 8 months. (Ali et al. Clin Br Ca, 2013). Clinical follow-up for additional patients is ongoing.

Conclusions: 96% of IBC cases harbored at least one alteration that suggests responsiveness to agents that are FDA approved or being studied in clinical trials. IBC cases also frequently had MYC amplifications (31%), but this may reflect a high percentage of TNBC-IBC cases with MYC amplifications (42%) in this series. Given the limited treatment options and poor prognosis of patients with metastatic IBC, the FoundationOne assay with comprehensive NGS-based genomic profiling has the potential to identify new treatment paradigms and address an unmet clinical need for this disease.

Citation Format: Norma A Palma, Siraj M Ali, Kai Wang, Juliann Chmeleiki, Gary Palmer, Deborah Morosini, Jeffrey S Ross, Vincent A Miller, Phil J Stephens, Massimo Cristofannilli. Genomic profiling by FoundationOne® analysis of inflammatory breast cancer cases reveals a high frequency of clinically relevant genomic alterations (GA) [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-14-02.

Prospective comprehensive genomic profiling of advanced gastric carcinoma cases reveals frequent clinically relevant genomic alterations and new routes for targeted therapies

BACKGROUND

Gastric cancer (GC) is a major global cancer burden and the second most common cause of global cancer-related deaths. The addition of anti-ERBB2 (HER2) targeted therapy to chemotherapy improves survival for ERBB2-amplified advanced GC patients; however, the majority of GC patients do not harbor this alteration and thus cannot benefit from targeted therapy under current practice paradigms.

MATERIALS AND METHODS

Prospective comprehensive genomic profiling of 116 predominantly locally advanced or metastatic (90.0%) gastric cancer cases was performed to identify genomic alterations (GAs) associated with a potential response to targeted therapies approved by the U.S. Food and Drug Administration or targeted therapy-based clinical trials.

RESULTS

Overall, 78% of GC cases harbored one clinically relevant GA or more, with the most frequent alterations being found in TP53 (50%), ARID1A (24%), KRAS (16%), CDH1 (15%), CDKN2A (14%), CCND1 (9.5%), ERBB2 (8.5%), PIK3CA (8.6%), MLL2 (6.9%), FGFR2 (6.0%), and MET (6.0%). Receptor tyrosine kinase genomic alterations were detected in 20.6% of cases, primarily ERBB2, FGFR2, and MET amplification, with ERBB2 alterations evenly split between amplifications and base substitutions. Rare BRAF mutations (2.6%) were also observed. One MET-amplified GC patient responded for 5 months to crizotinib, a multitargeted ALK/ROS1/MET inhibitor.

CONCLUSION

Comprehensive genomic profiling of GC identifies clinically relevant GAs that suggest benefit from targeted therapy including MET-amplified GC and ERBB2 base substitutions.

A Poorly Differentiated Malignant Neoplasm Lacking Lung Markers Harbors an EML4-ALK Rearrangement and Responds to Crizotinib

Suspected metastatic site lesions that are poorly differentiated present a diagnostic challenge when morphologic and immunohistochemical profiling cannot establish the primary tumor site. Here we present a patient diagnosed with both a malignant neoplasm in the lung and a right upper extremity (RUE) neoplasm of unclear histogenetic origin. Immunohistochemical staining performed on the latter specimen was inconclusive in determining the site of origin. Although the lung biopsy sample was insufficient for molecular testing, hybrid capture-based comprehensive genomic profiling (FoundationOne) identified an EML4-ALK rearrangement in the RUE lesion. Crizotinib treatment resulted in a major response in both the RUE and the lung lesions. This report illustrates the utility of comprehensive genomic profiling employed at the initial presentation of an unknown primary malignant neoplasm, which resulted in the front-line use of targeted therapy and a significant and sustained antitumor response.

Durable Response to Crizotinib in a MET-Amplified, KRAS-Mutated Carcinoma of Unknown Primary

Background

Carcinoma of unknown primary (CUP) accounts for 3–5% of all adult solid tumors. An extensive search for the anatomic site of origin is often undertaken in an attempt to tailor systemic treatment, but the latter often has limited efficacy – especially in the setting of an initial treatment failure. Molecularly targeted therapy is an emerging approach that may offer greater efficacy and less toxicity but is most likely to be effective when pairing a tumor harboring a sensitizing genomic alteration with an agent directed at the altered gene product. We report a patient with a CUP harboring a MET amplification with a complete metabolic response to crizotinib despite also harboring a KRAS mutation.

Methods

Ge-nomic profiling was performed using a clinical next-generation-sequencing-based assay, FoundationOne^®, in a CAP-accredited laboratory certified by Clinical Laboratory Improvement Amendments (Foundation Medicine, Cambridge, Mass., USA).

Results

The CUP harbored both MET amplification (16 copies) and a KRAS G12V mutation. The patient was treated with crizotinib, a MET inhibitor, and has experienced a complete normalization of tumor metabolic activity for more than 19 months. Conclusions: Genomic profiling of CUP may reveal clinically meaningful genomic alterations that can guide targeted therapy decision-making. The use of this approach should be studied prospectively as a strategy for the effective treatment of CUP patients and for avoiding resource-intensive workups to identify the tumor site of origin.